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ARS Home » Southeast Area » Tifton, Georgia » Crop Protection and Management Research » Research » Publications at this Location » Publication #335107
Title: Development and evaluation of a high density genotyping 'Axiom_Arachis' array with 58K SNPs for accelerating genetics and breeding in groundnut

Author
item PANDEY, MANISH - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item AGARWAL, GAURAV - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item KALE, SANDIP - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item CLEVENGER, JOSH - University Of Georgia
item NAYAK, SPURTHI - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item SRISWATHI, MANDA - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item CHITIKINENI, ANNAPURNA - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item CHAVARRO, CAROLINA - University Of Georgia
item CHEN, XIAOPING - Guangdong Academy
item BERTIOLI, DAVID - University Of Georgia
item Guo, Baozhu
item JACKSON, SCOTT - University Of Georgia
item OZIAS-AKINS, PEGGY - University Of Georgia
item VARSHNEY, RAJEEV - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/7/2016
Publication Date: 1/16/2017
Citation: Pandey, M.K., Agarwal, G., Kale, S.M., Clevenger, J., Nayak, S.N., Sriswathi, M., Chitikineni, A., Chavarro, C., Chen, X., Bertioli, D.J., Guo, B., Jackson, S.A., Ozias-Akins, P., Varshney, R.K. 2017. Development and evaluation of a high density genotyping 'Axiom_Arachis' array with 58K SNPs for accelerating genetics and breeding in groundnut. Scientific Reports. 7:40577 doi: 10.1038/srep40577.

Interpretive Summary: Groundnut or peanut is globally important crop that is cultivated in more than 100 countries and consumed in almost every country. Cultivated groundnut is an allotetraploid (2n = 4x = 40) species with two subgenomes (A and B) that complicates sharing of diversity of cultivated species with its wild diploid species. With the availability of draft genome sequences, re-sequencing and transcriptome sequencing of several accessions of tetraploid species as well as a number of diploid species accessions, we compiled a large number of SNPs and identified a comprehensive set of informative genome-wide SNPs. We report here the selection and development of 58K SNP array as well as its validation and utility in genetic diversity analysis in groundnut. This array is an important genomic resource for peanuts and especially peanut community that will be useful not only for accelerating genetics and breeding applications but also to understand evolutionary biology in Arachis species.

Technical Abstract: Single nucleotide polymorphisms (SNPs) are the most abundant DNA sequence variation in the genomes which can be used to associate genotypic variation to the phenotype. Therefore, availability of a high-density SNP array with uniform genome coverage can advance genetic studies and breeding applications. Here we report the development of a high-density SNP array “Axiom_Arachis” with 58K SNPs and its utility in groundnut genetic diversity study. In this context, from a total of 163,782 SNPs derived from DNA resequencing and RNA-sequencing of groundnut accessions and wild diploid ancestors, a total of 58,233 unique and informative SNPs were selected for developing the array. In addition to cultivated groundnuts (Arachis hypogea), fair representation was kept for other diploids (A. duranensis, A. stenosperma, A. cardenasii, A. magna and A. batizocoi). Genotyping of the groundnut ‘Reference Set’ containing 300 genotypes identified 44,424 polymorphic SNPs and genetic diversity analysis provided in-depth insights into the genetic architecture of this material. The availability of the high-density SNP array “Axiom_Arachis” with 58K SNPs will accelerate the process of high resolution trait genetics and molecular breeding in cultivated groundnut.